These
Java-based tools are capable of reading stacks of polygons described in svg vector format and arrange them in 3D space so that the
corresponding structures can be viewed and manipulated individually. An
additional excel (currently v. 1997-2003) file
maintains the structure abbreviations and their mapping to the terminology of
databases that provide supplementary information.
Here in particular we have manually drawn the cortical, striatal, thalamic and amygdaloid structures of the 151 frontal sections from the "Rhesus Monkey Brain in Stereotactic Coordinates" authored by Paxinos and colleagues in 1999. After loading the excel file and a set of the svg files, the view can be rotated, zoomed and individual brain structures be selected for identification and simple geometric measures. A stereotaxic grid is a display option.
The
abbreviations of the brain structures are mapped to entities recorded in the CoCoMac database of primate brain connectivity. Thereby one
can retrieve mapping and connectivity information for the selected structure as
text or connecting arrows.
The
CoCoMac-Paxinos-3D viewer is based on the Virtual Rat Brain code and is freely
available for download as an archive file under the GNU General Public License. The
software is provided 'as is', and we do not take any legal responsibility for
damages to potential copyright or patent holders.
You
are welcome to download the latest rar archive of the CoCoMac-Paxinos-3D viewer
including atlas templates, abbreviations and a pdf
file with instructions. In addition you will need both a recent java and a
subsequent java3D installation on your computer.
Further
information will be provided with the second edition of the "Rhesus Monkey
Brain in Stereotactic Coordinates" atlas (to be published later this year)
and in a forthcoming publication:
ˇ Kötter R., Reid A.T., Bezgin G. (2008) An Introduction
to the CoCoMac-Paxinos-3D Viewer. Chapter 4 in: Paxinos
G., Huang X.-F., Petrides M., Toga A.W. (eds.) The
Rhesus Monkey Brain in Stereotaxic Coordinates, 2nd
edition. Elsevier, San Diego, in press.
ˇ
Bezgin R., Reid A.T.,
Schubert D., Kötter R. (2008) Matching spatial with ontological brain entities
using integrated Java tools for visualization and database access. Neuroinformatics, in press.
For
feedback please send a message to g.bezgin [at] science.ru.nl.
09/2008
CoCoMac
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